Changeset 880 for trunk/python/asaplinefind.py
- Timestamp:
- 03/08/06 11:57:12 (20 years ago)
- File:
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- 1 edited
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trunk/python/asaplinefind.py (modified) (3 diffs)
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trunk/python/asaplinefind.py
r522 r880 16 16 print "No lines found!" 17 17 sc2=sc.poly_baseline(fl.get_mask(),7) 18 18 19 19 The algorithm involves a simple threshold criterion. The line is 20 20 considered to be detected if a specified number of consequtive … … 26 26 lowest variances across the spectrum (i.e. histogram equalization is 27 27 used to avoid missing weak lines if strong ones are present). For 28 bad baseline shapes it is rec commended to increase the threshold and28 bad baseline shapes it is recommended to increase the threshold and 29 29 possibly switch the averaging option off (see set_options) to 30 30 detect strong lines only, fit a high order baseline and repeat the line 31 search. 31 search. 32 32 33 33 """ 34 34 35 35 def __init__(self): 36 37 38 39 40 36 """ 37 Create a line finder object. 38 """ 39 self.finder = _asap.linefinder() 40 return 41 41 42 42 def set_options(self,threshold=1.7320508075688772,min_nchan=3, 43 43 avg_limit=8,box_size=0.2): 44 45 46 47 threshold a single channel S/N ratio above which the 48 49 50 51 min_nchan a minimal number of consequtive channels, 44 """ 45 Set the parameters of the algorithm 46 Parameters: 47 threshold a single channel S/N ratio above which the 48 channel is considered to be a detection 49 Default is sqrt(3), which together with 50 min_nchan=3 gives a 3-sigma criterion 51 min_nchan a minimal number of consequtive channels, 52 52 which should satisfy a threshold criterion to 53 54 55 56 57 53 be a detection. Default is 3. 54 avg_limit A number of consequtive channels not greater than 55 this parameter can be averaged to search for 56 broad lines. Default is 8. 57 box_size A running mean box size specified as a fraction 58 58 of the total spectrum length. Default is 1/5 59 Note: For bad baselines threshold should be increased, 60 61 62 undulations instead of real lines. 59 Note: For bad baselines threshold should be increased, 60 and avg_limit decreased (or even switched off completely by 61 setting this parameter to 1) to avoid detecting baseline 62 undulations instead of real lines. 63 63 """ 64 64 self.finder.setoptions(threshold,min_nchan,avg_limit,box_size) 65 66 65 return 66 67 67 def set_scan(self,scan,mask=None,edge=(0,0)): 68 """69 Set the 'data' (scantable) to work with.70 Parameters:71 scan: a scantable72 mask: an optional mask retreived from scantable73 edge: an optional number of channel to drop at74 the edge of spectrum. If only one value is75 specified, the same number will be dropped from76 both sides of the spectrum. Default is to keep77 all channels78 68 """ 79 if not scan: 80 raise RuntimeError, 'Please give a correct scan' 81 82 if isinstance(edge,int): 83 edge=(edge,) 69 Set the 'data' (scantable) to work with. 70 Parameters: 71 scan: a scantable 72 mask: an optional mask retreived from scantable 73 edge: an optional number of channel to drop at 74 the edge of spectrum. If only one value is 75 specified, the same number will be dropped from 76 both sides of the spectrum. Default is to keep 77 all channels 78 """ 79 if not scan: 80 raise RuntimeError, 'Please give a correct scan' 81 if not scan._check_ifs(): 82 raise RuntimeError, 'IFs with different numbers of channels are not yet supported' 83 84 if isinstance(edge,int): 85 edge=(edge,) 84 86 85 87 from asap import _is_sequence_or_number as _is_valid … … 89 91 a pair of integers specified as a tuple" 90 92 91 92 93 if len(edge)>2: 94 raise RuntimeError, "The edge parameter should have two \ 93 95 or less elements" 94 95 96 self.finder.setscan(scan,ones(scan.nchan()),tuple(edge))97 else: 98 99 return 96 if mask is None: 97 from numarray import ones 98 self.finder.setscan(scan,ones(scan.nchan(-1)),tuple(edge)) 99 else: 100 self.finder.setscan(scan,mask,tuple(edge)) 101 return 100 102 def find_lines(self,nRow=0): 101 102 103 104 105 106 103 """ 104 Search for spectral lines in the scan assigned in set_scan. 105 Current Beam/IF/Pol is used, Row is specified by parameter 106 A number of lines found will be returned 107 """ 108 return self.finder.findlines(nRow) 107 109 def get_mask(self,invert=False): 108 109 110 """ 111 Get the mask to mask out all lines that have been found (default) 110 112 111 112 113 Parameters: 114 invert if True, only channels belong to lines will be unmasked 113 115 114 115 116 116 Note: all channels originally masked by the input mask or 117 dropped out by the edge parameter will still be excluded 118 regardless on the invert option 117 119 """ 118 120 return self.finder.getmask(invert) 119 121 def get_ranges(self,defunits=True): 120 121 122 lines found. 122 """ 123 Get ranges (start and end channels or velocities) for all spectral 124 lines found. 123 125 124 125 126 127 if False, the range will be expressed in channels 128 129 130 131 132 126 Parameters: 127 defunits if True (default), the range will use the same units 128 as set for the scan (e.g. LSR velocity) 129 if False, the range will be expressed in channels 130 """ 131 if (defunits): 132 return self.finder.getlineranges() 133 else: 134 return self.finder.getlinerangesinchannels()
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